Main
Peng Zhou
Post Doctoral Associate at University of Minnesota. Using a combination of classical genetics, comparative genomics and multi-omics approaches, I want to understand the regulatory mechanism of gene expression during plant development and under stress conditions. My research interests also include building plant gene regulatory networks, training machine learning models to predict temporal/spatial gene expression patterns, as well as understanding the molecular mechanism giving rise to heterosis.
Education
Ph.D. Plant Pathology & Bioinformatics
University of Minnesota, Twin Cities
St. Paul US
2015 - 2009
- Thesis: Defense-related gene families in the model legume, Medicago truncatula: computational analysis, pan-genome characterization, and structural variation
- Advisor: Prof. Neivn D. Young
M.S. Forensic Medicine
Xi’an Jiaotong University
Xi’an CN
2009 - 2007
- Thesis: Dissection of Common Mitochondrial Haplogroups using Coding Region SNPs
- Advisor: Prof. Shengbin Li
B.E. Biological Engineering & Computer Science and Technology
Xi’an Jiaotong University
Xi’an CN
2007 - 2003
Research Experience
Post Doctoral Associate
Department of Plant and Microbial Biology
University of Minnesota, Twin Cities
present - 2016
- Elucidate hybrid vigor using multi-omics approach; data mining on functional gene regulations; elucidation of transcriptional regulatory differences underlying stress response; integrating multi-omics dataset for transcriptional network construction.
- Nathan M. Springer Lab
AgroInformatics Analyst
Department of Applied Economics
University of Minnesota, Twin Cities
2016 - 2015
- Design and implement a generic database and user interface for storing genotyping, breeding and phenotyping information for soybean breeding programs.
Research Assistant
Department of Plant Pathology
University of Minnesota, Twin Cities
2015 - 2009
- Medicago truncatula reference genome assembly, characterization of structural variation in the population, pan-genome construction
Teaching Experience
PLPA5001: Introductory Plant Pathology
Department of Plant Pathology
University of Minnesota, Twin Cities
2012 - 2011
- Teach laboratory sessions, lead discussion sections, answer questions and grade examinations.
Representative Publications
- Citation = 2138
- H-index = 16
- I10-index = 17
Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize
bioRxiv. 2021. p. 2021.01.15.426829.
N/A
2021
- Zhou P, Enders TA, Myers ZA, Magnusson E, Crisp PA, Noshay J, et al.
Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions
Plant Cell. 2020, 32: 1377-1396.
N/A
2020
- Zhou P, Li Z, Magnusson E, Cano FAG, Crisp PA, Noshay J, Grotewold E, HirschC, Briggs SP, Springer NM
- Impact Factor = 9.618
Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development
Molecular Plant. 2019, 12: 410-425.
N/A
2019
- Zhou P, Hirsch CN, Briggs SP, Springer NM
- Impact Factor = 12.084
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model
BMC Genomics. 2017, 18: 578.
N/A
2017
- Moll KM*, Zhou P*, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, et al
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes
BMC Genomics. 2017, 18: 261.
N/A
- Zhou P, Silverstein KAT, Ramaraj T, Guhlin J, Denny R, Liu J, et al
Other Publications
Widespread imprinting of transposable elements and young genes in the maize endosperm
PLoS Genetics. In Press.
N/A
2021
- Anderson SN, Zhou P, Higgins K, Brandvain Y, Springer NM
Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons
Genetics. 2021, 217: 1–13.
N/A
- Noshay JM, Marand AP, Anderson SN, Zhou P, Guerra MKM, Lu Z, et al
Single-parent expression drives dynamic gene expression complementation in maize hybrids
Plant Journal. 2021, 105: 93–107.
N/A
- Li Z, Zhou P, Della Coletta R, Zhang T, Brohammer AB, H O’Connor C, et al.
The antagonistic MYB paralogs RH1 and RH2 govern anthocyanin leaf markings in Medicago truncatula
New Phytologist. 2021, 229: 3330–3344.
N/A
- Wang C, Ji W, Liu Y, Zhou P, Meng Y, Zhang P, et al.
Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes
Proc Natl Acad Sci U S A.. 2020, 117: 23991–24000.
N/A
2020
- Crisp PA, Marand AP, Noshay JM, Zhou P, Lu Z, Schmitz RJ, et al.
Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids
Plant Physiol. 2020, 182: 318-331.
N/A
- Crisp PA, Hammond R, Zhou P, Vaillancourt B, Lipzen A, Daum C, et al
Monitoring the interplay between transposable element families and DNA methylation in maize
PLoS Genetics. 2019, 15: e1008291.
N/A
2019
- Noshay JM, Anderson SN, Zhou P, Ji L, Ricci W, Lu Z, et al
Transposable elements contribute to dynamic genome content in maize
Plant Journal. 2019, 100: 1052-1065.
N/A
- Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O’Connor CH, et al
Hybrid assembly with long and short reads improves discovery of gene family expansions
BMC Genomics. 2017, 18: 541.
N/A
2017
- Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, et al
ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding
BMC Bioinformatics. 2017, 18: 367.
N/A
- Guhlin J, Silverstein KAT, Zhou P, Tiffin P, Young ND
Exploring structural variants in environmentally sensitive gene families
Curr Opin Plant Biol. 2016, 30: 19–24.
N/A
2016
- Young ND, Zhou P, Silverstein KA
Genomic signature of adaptation to climate in Medicago truncatula
Genetics. 2014, 196: 1263–1275.
N/A
2014
- Yoder JB, Stanton-Geddes J, Zhou P, Briskine R, Young ND, Tiffin P
Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula
Molecular Ecology. 2011, 108: E864-70.
N/A
2013
- Paape T, Bataillon T, Zhou P, J Y Kono T, Briskine R, Young ND, et al
Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)
BMC Bioinformatics. 2013, 14: 335.
N/A
- Zhou P, Silverstein KA, Gao L, Walton JD, Nallu S, Guhlin J, et al
Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula
Proc Natl Acad Sci U S A. 2013, 22: 3525–3538.
N/A
- Branca A, Paape TD, Zhou P, Briskine R, Farmer AD, Mudge J, et al
Fine-scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome)
Genome Biol Evol. 2012, 4: 726–737.
N/A
2012
- Paape T, Zhou P, Branca A, Briskine R, Young N, Tiffin P
The Medicago genome provides insight into the evolution of rhizobial symbioses
Nature. 2011, 480: 520-524.
N/A
2011
- Young ND, Debellé F, Oldroyd GED, … , Zhou P, …, et al
- ESI Highly Cited Paper
Professional service
Reviewer for journals
N/A
N/A
- Plant Biotechnology Journal
- Plant Science
- The Plant Genome
- Plant Direct
- Crop Science
Conference presentations
Meta gene regulatory networks in maize refine functionally relevant regulatory interactions
Plant and Animal Genome XXVIII Conference
San Diego, CA
2020
Exploring Functional Transcriptomics using Gene Regulatory Networks in Maize.
61st Annual Maize Genetics Conference
St. Louis, MO
2019
Documenting the Manifestations of Heterosis in Co-expression Networks for Maize
Plant and Animal Genome XXVI Conference
San Diego, CA
2018
The Medicago Pan-Genome Reveals Large-scale Variation
Plant and Animal Genome XXII Conference
San Diego, CA
2014
Detecting secreted peptides in plants using SPADA (Secreted Peptide Alignment Discovery Algorithm)
Plant and Animal Genome XXI Conference
San Diego, CA
2013
Population-Scale Deep Sequencing Reveals Extensive Structural Variation in Medicago species
Minnesota Supercomputing Institute Research Exhibition
Minneapolis, MN
2011
Genome Distribution and Population Genetics of Nodule-Specific Cysteine-Rich (NCR) Peptides in Medicago
Plant and Animal Genome XIX Conference
San Diego, CA
A Medicago truncatula Hapmap as a Platform for Exploring the Genetics of Symbiosis
Plant and Animal Genome XVIII Conference
San Diego, CA
2010
Invited Presentations/Seminars
Co-expression based Gene Regulatory Networks Predict Functional Interactions in Maize
N/A
China Agriculture University, Beijing
2019
Transcriptome Dynamics in Maize
N/A
Huazhong Agriculture University, Wuhan
Toward a Medicago Pan-genome: Assembling and Comparing Multiple Genomes
Medicago truncatula Workshop
Noble Research Institute, Ardmore
2016
Assembling and Comparing Multiple High-Quality Medicago Genomes
N/A
Chinese Academy of Agricultural Sciences (CAAS), Beijing